Monoclonal antibodies against the 60 kDa heat shock protein (HSP-60) and against ubiquitin (UB) were used to study the expression of these proteins in muscle samples from patients with qualitative and quantitative alterations of mitochondrial DNA (mtDNA). We found an enhanced expression of HSP-60 and UB that was preferentially localized in ragged-red fibers (RRFs). HSP-60 may act as a protein repair enzyme catalyzing the refolding of misfolded proteins in the matrix of mitochondria of RRFs. On the other hand, UB could promote the elimination of abnormal proteins by its covalent interaction to substrates.